Category Archives: Animal microbiome

January 17, 2024

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Pregnancy and early life

Human milk cream alters intestinal microbiome of preterm infants: a prospective cohort study – Adeniyi-Ipadeola et al. – Pediatric Research

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Buzun et al. – Cell Host & Microbe

Multi-site human microbiome

[DATA]Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults – Rashidi et al. – Scientific Data

Human respiratory microbiome

[REVIEW]Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies – Cauwenberghs et al. – Cell Reports Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling – Lai et al. – npj Biofilms and Microbiomes volume

Nonylphenol induces depressive behavior in rats and affects gut microbiota: A dose–dependent effect – Pan et al. – Environmental Pollution

Animal microbiome (for animals in the wild)

Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity – Kong et al. – Microbiome

Plant, root, and soil microbiome

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet – Alahmad et al. – Microbiome

Biogeographic survey of soil bacterial communities across Antarctica – Varliero et al. – Microbiome

Microbes in space

[PREPRINT]Testing microbial biomining from asteroidal material onboard the International Space Station – Santomartino et al. – bioRxiv

Bioinformatics

[PREPRINT]AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods – Wei et al. – bioRxiv

Techniques

Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly – Hu et al. – Scientific Reports

December 15, 2023

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Today’s digest features house mice gut microbiome, infant gut DNA bacteriophage strain persistence, maternal gut microbiome in pregnancy, and more.

Do not miss Francine Marques’s opinion on rethinking culture to unlock the potential of research.

See you at #MVIF next week!

Respiratory microbiome

Review: Winds of change a tale of: asthma and microbiome – David Galeana-Cadena – Frontiers in Microbiology

Gut microbiome

Review: The maternal gut microbiome in pregnancy: implications for the developing immune system – Omry Koren – Nature Reviews Gastroenterology & Hepatology

Bioactive glycans in a microbiome-directed food for children with malnutrition – Matthew C. Hibberd – Nature

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients – Zixuan Xie – Microbiome

Gut microbiota-related metabolite alpha-linolenic acid mitigates intestinal inflammation induced by oral infection with Toxoplasma gondii – Jing Yang – Microbiome

Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont – Peter Kuffa – Cell Host & Microbe

Animal microbiome

Subspecies divergence, hybridisation and the spatial environment shape phylosymbiosis in the microbiome of house mice – Susana C. M. Ferreira – bioRxiv

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers – Gilles L. C. Baud – Genome Biology

Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird – Martta Liukkonen – bioRxiv

Plant-Root-Soil microbiome

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota – Nathan Vannier – Nature Communications

Virome

Infant gut DNA bacteriophage strain persistence during the first 3 years of life – Yue Clare Lou – Cell Host & Microbe

Techniques

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities – Patrick Müller – Nature Protocols

Bioinformatics

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes – James P.J. Chong – bioRxiv

December 6, 2023

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Human salivary microbiome

Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer – de Medeiros et al. – Microbiome

Human skin microbiome

[PREPRINT]Commensal skin bacteria exacerbate inflammation and delay skin healing – Khadka et al. – bioRxiv

Human vaginal microbiome

Integrating compositional and functional content to describe vaginal microbiomes in health and disease – Holm et al. – Microbiome

Comparison of vaginal microbiota between women with inflammatory bowel disease and healthy controls – Bar et al. – PLOS One

Human gut microbiome

Engraftment of essential functions through multiple fecal microbiota transplants in chronic antibiotic-resistant pouchitis—a case study using metatranscriptomics – Deng et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio) – Teng et al – Microbiome

Animal microbiome (for animals in the wild)

Diversity of gut microbiome in Rocky Mountainsnail across its native range – Chalifour, Elder & Li – PLOS One

[PREPRINT]Testing the effectiveness of a commercially sold probiotic on restoring the gut microbiota of honey bees: a field study – Damico et al. – bioRxiv

Core gut microbes Cloacibacterium and Aeromonas associated with different gastropod species could be persistently transmitted across multiple generations – Lin et al. – Microbiome

Plant, root, and soil microbiome

Effects of multiple N, P, and K fertilizer combinations on strawberry growth and the microbial community – Bai et al. – PLOS One

Comparison of microbial community assemblages in the rhizosphere of three Amaranthus spp. – Chee-Sanford & Connor – PLOS One

Bioinformatics

Phantom oscillations in principal component analysis – Shinn – PNAS
This phenomenon is not new (e.g. know as horseshoe effect) but Shinn gives a very understandable explanation.

The MAGMA pipeline for comprehensive genomic analyses of clinical Mycobacterium tuberculosis samples – Heupink et al. – PLOS Computational Biology

[PREPRINT]metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis – Sun et al. – bioRxiv

[PREPRINT]MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics – Ma, Thairu & Sankaran

November 28, 2023

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Pregnancy and early life

[PREPRINT]Delivery mode impacts gut bacteriophage colonization during infancy – Subramanian et al. – medRxiv

Human oral microbiome

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries – Alyousef et al. – BMC Oral Health

Human gut microbiome

Gastric coinfection with thiopeptide-positive Cutibacterium acnes decreases FOXM1 and pro-inflammatory biomarker expression in a murine model of Helicobacter pylori-induced gastric cancer – Lunger et al. – Microbiology Spectrum

[REVIEW]Butterflies in the gut: the interplay between intestinal microbiota and stress – Lai et al. – Journal of Biomedical Science

[REVIEW]Genetics, Nutrition, and Health: A New Frontier in Disease Prevention – Agrawal et al. – Journal of the American Nutrition Association

Age-dependent changes in the gut microbiota and serum metabolome correlate with renal function and human aging – Sun et al. – Aging Cell

The changes of gut microbiota and metabolites in different drug-induced liver injuries – Zhu et al. – Journal of Medical Microbiology

[PREPRINT]The differing prevalences of propionate and butyrate producing bacteria in the human gut microbiota – Christensen et al. – bioRxiv

[PREPRINT]The Parkinson’s drug entacapone disrupts gut microbiome homeostasis via iron sequestration – Pereira et al. – bioRxiv

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Mutual modulation of gut microbiota and the immune system in type 1 diabetes models – Rosell-Mases et al. – Nature Communications

[PREPRINT]Microbiota-dependent early life programming of gastrointestinal motility – Frith et al. – bioRxiv

Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis – Gurczynski et al. – JCI insight

High-altitude and low-altitude adapted chicken gut-microbes have different functional diversity – Bhagat et al. – Scientific Reports

Animal microbiome (for animals in the wild)

Introducing an environmental microbiome to axenic Aedes aegypti mosquitoes documents bacterial responses to a blood meal – LaReau et al. – Applied and Environmental Microbiology

Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer – Zhuang et al. – Microbiology Spectrum

Plant, root, and soil microbiome

[PREPRINT]Global patterns in gene content of soil microbiomes emerge from microbial interactions – Crocker et al. – bioRxiv

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India – Brar et al. – Journal of Genetic Engineering and Biotechnology

Bioinformatics

mb-PHENIX: Diffusion and Supervised Uniform Manifold Approximation for denoising microbiota data – Padron-Manrique et al. – Bioinformatics

Facilitating bioinformatics reproducibility with QIIME 2 provenance Replay – Keefe et al. – PLOS Computational Biology

Techniques

High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ – Jin, Yamamoto & Shiroguchi

November 10, 2023

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Read about new species discovered in the female genitourinary tract Lactobacillus isalae, Gardnerella pickettii and Gardnerella greenwoodii, and important UTI and other latest microbiome science news.
Happy Friday! And see you next week at MVIF!

Urinary microbiome

A human urothelial microtissue model reveals shared colonization and survival strategies between uropathogens and commensals – Carlos Flores – Science Advances

Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome – Márcia Sousa – International Journal of Systematic and Evolutionary Microbiology

Vaginal microbiome

Lactobacillus isalae sp. nov., isolated from the female reproductive tract – Tom Eilers – International Journal of Systematic and Evolutionary Microbiology

Identification of a DNA-cytosine methyltransferase that impacts global transcription to promote group B streptococcal vaginal colonization – Haider S. Manzer – mBio

Gut microbiome

Aggression: A gut reaction? The effects of the gut microbiome on aggression – Atara Uzan-Yulzari – bioRxiv

Oral microbiome

Establishment of tongue microbiota by 18 months of age and determinants of its microbial profile – Shinya Kageyama – mBio

Animal microbiome

Pet cats may shape the antibiotic resistome of their owner’s gut and living environment – Yiwen Yang – Microbiome

The impact of kit, environment and sampling contamination on the observed microbiome of bovine milk – Christopher J Dean – bioRxiv

Animal experiments

Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease – Lola Holcomb – mSystems

Daily fluctuation of colonic microbiome in response to nutrient substrates in a pig model – Hongyu Wang – npj Biofilms and Microbiomes

Water microbiome

Assessing the impact of anti-microbial showerheads on the prevalence and abundance of opportunistic pathogens in shower water and shower water-associated aerosols – Sarah Pitell, Sarah-Jane Haig – Frontiers in Microbiomes

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – bioRxiv

Technique

A high-throughput and low-waste viability assay for microbes – Christian T. Meyer – Nature Microbiology

Bioinformatics

Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses – Saioa Manzano-Morales – Genome Biology

ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool – Hoon Je Seong – Briefings in Bioinformatics


October 18, 2023

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Human gut microbiome

Association between gut microbiota and influenza: a bidirectional two-sample mendelian randomization study – Xu et al. – BMC Infectious Diseases

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

LACC1 regulates changes in the intestinal flora in a mouse model of inflammatory bowel disease – Xu & Wang – BMC Gastroenterology

Animal microbiome (for animals in the wild)

[PREPRINT]Sex-specific gut bacteria manipulation impacts offspring production in the honeybee parasite small hive beetle, Aethina tumida Murray – Biswas et al. – bioRxiv

Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite – Sinotte et al. – Proc. R. Soc. B

Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing – Klinsawat et al. – Scientific Reports

Temporal and spatial variations in body mass and thermogenic capacity associated with alterations in the gut microbiota and host transcriptome in mammalian herbivores – Ren et al. – Science of The Total Environment

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system – Rajeev et al. – Scientific Data

Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome – Bertagnolli et al. – ISME Communications

Parasites, Phages and viruses

Effects of heat tolerance on the gut microbiota of Sarcophaga peregrina (Diptera: Sarcophagidae) and impacts on the life history traits – Ren et al. – Parasites & Vectors

Bioinformatics / Techniques

[PREPRINT]Comprehensive Identification of Pathogenic Microbes and Antimicrobial Resistance Genes in Food Products Using Nanopore Sequencing-Based Metagenomics – Wing-Tung et al. – bioRxiv

Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses – Hertel et al. – Cell Reports Methods

Rank selection for non-negative matrix factorization – Cai, Gu & Kenney

October 13, 2023

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Today’s digest features the Chinese Gut Microbiome Resource, plate readers in the anaerobic chamber, seasonal stability of sponge microbiomes, and more.

Also, you can support the outreachy bugsigdb project by sharing your study to be curated (more info here https://www.outreachy.org/apply/project-selection/#bioconductor or contact me). See you at #MVIF next week!

General

From hype to hope: considerations in conducting robust microbiome science – Amelia J McGuinness – Brain, Behavior, and Immunity

Global

Unraveling the functional dark matter through global metagenomics – Georgios A. Pavlopoulos – Nature

Human gut microbiome

Integration of 168,000 samples reveals global patterns of the human gut microbiome – Richard J. Abdill – bioRxiv

Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets – Anna C. Salvador – Microbiome

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects – Pan Huang – bioRxiv

Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index – Sofía Tesolato – PlosOne

Tracking gut microbiome and bloodstream infection in critically ill adults – Christopher H. Gu – PlosOne

Human milk

Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy – Martin F. Laursen & Henrik M. Roager – The ISME Journal

Antibiotic Resistome

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments – Jessica Subirats – Applied and Environmental Microbiology

Plant microbiome

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods – Sabin Khana – bioRxiv

Animal microbiome

Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa – Claire E. Lamb & Joy E. M. Watts – Environmental Microbiome

An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management – Rita A. H. Hoving-Bolink – PlosOne

Technique

Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers – Oona L.O. Snoeyenbos-West – bioRxiv

Bioinformatics

On the relationship between protist metabarcoding and protist metagenome-assembled genomes – Daryna Zavadska – bioRxiv

Track, Analyze, Visualize: Unravel Your Microbiome’s Temporal Tale with MicrobiomeStat – Chen Yang & MicrobiomeStat team

October 11, 2023

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General microbiome

Major data analysis errors invalidate cancer microbiome findings – Gihawi et al. – mBio

Relative abundance data can misrepresent heritability of the microbiome – Bruihning et al. – Microbiome

Human gut microbiome

Discrimination exposure impacts unhealthy processing of food cues: crosstalk between the brain and gut – Zhang et al. – Nature Mental Health

[REVIEW]The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective – Leigh et al. – The Journal of Physiology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]The role of family and environment in determining the skin microbiome of captive aquatic frogs, Xenopus laevis – Chapman et al. – bioRxiv

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Bioinformatics/Techiques

[PREPRINT]MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples – Xu et al. – bioRxiv

[PREPRINT]Insertion sequence driven evolution of the microbiota revealed by a novel metagenomics pipeline – Kirsch, Hryckowian & Duerkop

[PREPRINT]A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics – Eisenhofer et al. – bioRxiv

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Zhang et al. – Applied and Environmental Microbiology

[PERSPECTIVE]Challenges and opportunities in sharing microbiome data and analyses – Huttenhower, Finn & McHardy – Nature Microbiology

October 4, 2023

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General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Statistically learning the functional landscape of microbial communities – Skwara et al. – Nature Ecology & Evolution

Human skin microbiome

Skin microbiota secretomes modulate cutaneous innate immunity against Borrelia burgdorferi s.s – Baquer et al. – Scientific Reports

Human gut microbiome

Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort – Galperine et al. – BMC Infectious Diseases

Association Between Bowel-Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome – Ma et al. – Neurology

[REVIEW]The gut microbiome tango in the progression of chronic kidney disease and potential therapeutic strategies – Tang, Yu & Pan – Journal of Translational Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Microbiota-gut-brain axis drives overeating disorder – Fan et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics – Wang et al. – Animal Microbiome

Plant, root, and soil microbiome

Using wasps as a tool to restore a functioning vine grape mycobiota and preserve the mycobial “terroir” – Di Paola et al. – Scientific Reports

Soil microbes mediate the effects of resource variability on plant invasion – Zhang et al. – Ecology

Bioinformatics

[PREPRINT]Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes – Zou et al. – bioRxiv

[PREPRINT]BATTER: Accurate Prediction of Rho-dependent and Rho-independent Transcription Terminators in Metagenomes – Jin et al. – bioRxiv

[PREPRINT]Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles – Chang et al. – bioRxiv

Techniques

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution – Nino et al. – Nature Protocols

September 20, 2023

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General microbiome

Frequency of change determines effectiveness of microbial response strategies – Li et al. – The ISME Journal

Human gut microbiome

Social and psychological adversity are associated with distinct mother and infant gut microbiome variations – Warner et al. – Nature Communications

Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua – Mills et al. – Microbiome

Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts – Hansen et al. – Scientific Reports

The Impacts of Fecal Microbiota Transplantation from Same Sex on the Symptoms of Ulcerative Colitis Patients – Shang et al. – Polish Journal of Microbiology

Animal microbiome (for animals in the wild)

Transcriptomic, 16S ribosomal ribonucleic acid and network pharmacology analyses shed light on the anticoccidial mechanism of green tea polyphenols against Eimeria tenella infection in Wuliangshan black-boned chickens – Song et al. – Parasites & Vectors

Dityrosine Aggravates Hepatic Insulin Resistance in Obese Mice by Altering Gut Microbiota and the LPS/TLR4/NF-κB Inflammatory Pathway – Ding et al. – Molecular Nutrition & Food Research

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

[REVIEW]Microbiome-assisted restoration of degraded marine habitats: a new nature-based solution? – Corinaldesi et al. – Frontiers in Marine Science

Bioinformatics

[PREPRINT]Comparison of computational methods for host removal and classification of mycobacteria from clinical metagenomic data – Hall & Coin – bioRxiv